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I'm running OmniGraffle 5.4.4 (v139.18 r187838). I have a strange alignment issue when exporting to PDF. If everything is lined up properly in the OmniGraffle project, it ends up off by quite a few pixels in the PDF. This doesn't happen with everything, generally just shapes and text (lines are OK, for example), and there doesn't seem to be a standard offset/direction that it adheres to either, it's just sort of random. The following objects are quite small (10 pixels wide), it doesn't seem to be as much of an issue with larger objects.

Here is an example screenshot from the OmniGraffle project:

Here is the corresponding item in the exported PDF:

It's been bugging me to upgrade (for a price, of course). Does anybody know if the upgrade will fix this (or of any other fix for it)?

I guess I spoke too soon. The issue is indeed not present, but it has been replaced by a new issue wherein shape strokes on small shapes get misaligned in PDF exports. I suppose I'll just need to find a way to deal with that.

Yes, there are definitely alignment issues with PDF export, even with the very latest version 6.0.5.

E.g.Take the blue arrow from the "Connections" template, rotate it 270 degrees, decrease the opacity of either one of the colors in the linear fill. When you export as a PDF vector image the fill will appear unrotated, and the outline will be rotated.